The differences in plant diversity and plant community structure in the Water-Level-Fluctuating Zone (WFLZ) of the Three Gorges Reservoir (TGR) were studied in present study. As far as α diversity was concerned, significant differences in plant species richness and equitability between upside and middle side of the WFLZ were not found. The Plant species richness in the downside of the WFLZ is lower than that of the upside and middle side. Compared with the the upside and middle side, the highest PIE (population encounter incidence) in the downside of the WFLZ manifested that the strongest interdependency among the plant species was existed. As far as β diversity was concerned, the substitution of plant species was homogeneous with the decrease of altitude in the WFLZ from upside to downside. Significant differences in β diversity were not found among different studied sites, but found among different altitude within the same studied site. Compared with the upside of the WFLZ, the plant community structural stability of downside is highesr and the middle side is lower. In the upside of the WFLZ, the mildest flooding stress is benefit for the reciprocal competition of all kinds of species, and then many plant species can survive and be belonged to competitive species. The weeds which possessed higher competitive capacity formed their dominant communities. In the downside of the WFLZ, the survived species were screened by the strongest flooding stress. The plants belonging to tolerant species, which can tolerate high intensity flooding stress, could survive and form their dominance community. The flooding stress in the middle side of the WFLZ is intermediate between upside and e downside of the WFLZ. The plants in the middle side of the WFLZ were suffered from species reciprocal competitive stress and flooding stress. The plant species possessed stronger competitive capacity and flooding tolerance formed their dominance community. Therefore, the stability of the plant community was relative weak, and the plants formed their co-dominated communities. Under the present conditions, the plant community composition in the downside of the WFLZ was single than that of the upside and middle side. However, it is estimated that the plant community composition in the upside and middle side of the WFLZ will become single gradually with the stabilization to 175 meters of water-retention level.